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Protein

Probable pectate lyase 18

Gene

At4g24780

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

Functioni

Catalytic activityi

Eliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends.

Cofactori

Ca2+By similarityNote: Binds 1 Ca2+ ion. Required for its activity.By similarity

Pathwayi: pectin degradation

This protein is involved in step 2 of the subpathway that synthesizes 2-dehydro-3-deoxy-D-gluconate from pectin.
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. Pectinesterase (PMEPCRA), Pectinesterase (AXX17_At2g44790), Pectinesterase (AXX17_At5g50300), Pectinesterase (AXX17_At5g20800), Pectinesterase (AXX17_At5g45990), Pectinesterase (AXX17_At3g55110), Pectinesterase (AXX17_At1g24390), Pectinesterase (AXX17_At3g06710), Pectinesterase (AXX17_At1g48300), Pectinesterase (AXX17_At4g00230), Pectinesterase (AXX17_At5g50310), Pectinesterase (AXX17_At2g33420), Pectinesterase (AXX17_At3g31890), Pectinesterase (PMEPCRF), Pectinesterase (At3g10720), Putative pectinesterase 10 (PME10), Putative pectinesterase 11 (PME11), Probable pectinesterase/pectinesterase inhibitor 12 (PME12), Probable pectinesterase/pectinesterase inhibitor 13 (PME13), Putative pectinesterase 14 (PME14), Probable pectinesterase 15 (PME15), Probable pectinesterase/pectinesterase inhibitor 16 (PME16), Probable pectinesterase/pectinesterase inhibitor 17 (PME17), Pectinesterase/pectinesterase inhibitor 18 (PME18), Probable pectinesterase/pectinesterase inhibitor 19 (PME19), Pectinesterase 1 (PME1), Probable pectinesterase/pectinesterase inhibitor 20 (PME20), Probable pectinesterase/pectinesterase inhibitor 21 (PME21), Putative pectinesterase/pectinesterase inhibitor 22 (PME22), Probable pectinesterase/pectinesterase inhibitor 23 (PME23), Putative pectinesterase/pectinesterase inhibitor 24 (PME24), Probable pectinesterase/pectinesterase inhibitor 25 (PME25), Putative pectinesterase/pectinesterase inhibitor 26 (PME26), Putative pectinesterase/pectinesterase inhibitor 28 (PME28), Probable pectinesterase 29 (PME29), Pectinesterase 2 (PME2), Probable pectinesterase 30 (PME30), Pectinesterase 31 (PME31), Probable pectinesterase/pectinesterase inhibitor 32 (PME32), Probable pectinesterase/pectinesterase inhibitor 33 (PME33), Probable pectinesterase/pectinesterase inhibitor 34 (PME34), Probable pectinesterase/pectinesterase inhibitor 35 (PME35), Probable pectinesterase/pectinesterase inhibitor 36 (PME36), Probable pectinesterase/pectinesterase inhibitor VGDH2 (VGDH2), Putative pectinesterase/pectinesterase inhibitor 38 (PME38), Probable pectinesterase/pectinesterase inhibitor 39 (PME39), Pectinesterase/pectinesterase inhibitor 3 (PME3), Probable pectinesterase/pectinesterase inhibitor 40 (PME40), Probable pectinesterase/pectinesterase inhibitor 41 (PME41), Probable pectinesterase/pectinesterase inhibitor 42 (PME42), Putative pectinesterase/pectinesterase inhibitor 43 (PME43), Probable pectinesterase/pectinesterase inhibitor 44 (PME44), Putative pectinesterase/pectinesterase inhibitor 45 (PME45), Probable pectinesterase/pectinesterase inhibitor 46 (PME46), Probable pectinesterase/pectinesterase inhibitor 47 (PME47), Probable pectinesterase 48 (PME48), Probable pectinesterase 49 (PME49), Pectinesterase 4 (PME4), Probable pectinesterase 50 (PME50), Probable pectinesterase/pectinesterase inhibitor 51 (PME51), Putative pectinesterase 52 (PME52), Probable pectinesterase 53 (PME53), Probable pectinesterase/pectinesterase inhibitor 54 (PME54), Probable pectinesterase 55 (PME55), Probable pectinesterase 56 (PME56), Putative pectinesterase 57 (PME57), Probable pectinesterase/pectinesterase inhibitor 58 (PME58), Probable pectinesterase/pectinesterase inhibitor 59 (PME59), Pectinesterase 5 (PME5), Probable pectinesterase/pectinesterase inhibitor 60 (PME60), Probable pectinesterase/pectinesterase inhibitor 61 (PME61), Pectinesterase QRT1 (QRT1), Putative pectinesterase 63 (PME63), Probable pectinesterase/pectinesterase inhibitor 64 (PME64), Probable pectinesterase 66 (PME66), Probable pectinesterase 67 (PME67), Probable pectinesterase 68 (PME68), Probable pectinesterase/pectinesterase inhibitor 6 (PME6), Probable pectinesterase/pectinesterase inhibitor 7 (PME7), Probable pectinesterase 8 (PME8), Pectinesterase PPME1 (PPME1), Pectinesterase (AXX17_At3g36460), Pectinesterase (AXX17_At4g06570), Pectinesterase (AXX17_At3g14900), Pectinesterase (AXX17_At3g30550), Pectinesterase (At3g14310), Pectinesterase (AXX17_At1g11890), Pectinesterase (AXX17_At4g18720), Pectinesterase (At4g15980), Pectinesterase (At3g49220), Pectinesterase (AXX17_At2g22270), Pectinesterase (AXX17_At4g38050), Uncharacterized protein (AXX17_At3g05180), Pectinesterase (AXX17_At5g47900), Pectinesterase, Pectinesterase (AXX17_At5g19650), Pectinesterase (AXX17_At3g43380), Pectinesterase (AXX17_At4g02900), Pectinesterase (AXX17_At2g42790), Pectinesterase (AXX17_At3g10570), Pectinesterase (AXX17_At3g56460), Plant invertase/pectin methylesterase inhibitor superfamily (At3g49220), Pectinesterase (AXX17_At4g02940), Pectinesterase (AXX17_At1g11900), PME26 (AXX17_At3g14890), Uncharacterized protein (AXX17_At5g27870), Uncharacterized protein (AXX17_At5g64270), Pectinesterase (AXX17_At1g04730), Pectinesterase (AXX17_At3g41380), Pectinesterase (AXX17_At5g04430), Pectinesterase, Pectinesterase (F14I3.7), Pectinesterase (AXX17_At2g22280), Pectinesterase, Pectinesterase (AXX17_At5g52320), Pectinesterase (AXX17_At2g33420), Pectinesterase, Pectinesterase (AXX17_At1g11920), Pectinesterase (AXX17_At2g40510), Pectinesterase (At5g20860), Pectinesterase (AXX17_At3g26070), Pectinesterase (AXX17_At3g10560), Pectinesterase (AXX17_At1g48290), Pectinesterase (AXX17_At1g01970), Pectinesterase (AXX17_At2g44780), Pectinesterase (AXX17_At4g38040), Pectinesterase (AXX17_At2g33410), Pectinesterase (AXX17_At5g04420), Pectinesterase (AXX17_At3g05190), Pectinesterase (AXX17_At3g53530), Pectinesterase (AXX17_At4g02930), Pectinesterase (AXX17_At3g17940), Pectinesterase (AXX17_At2g45340), Plant invertase/pectin methylesterase inhibitor superfamily (At5g09760), Pectinesterase (At5g26810), Pectinesterase (PME44), Pectinesterase (At1g53840)
  2. Pectate lyase (AXX17_At3g06910), Pectate lyase (At3g27400), Pectate lyase (AXX17_At3g26200), Pectate lyase (AXX17_At3g09180), Pectate lyase (AXX17_At3g49450), Pectate lyase (AXX17_At3g49720), Pectate lyase (AXX17_At4g25610), Putative pectate lyase 14 (At4g13210), Probable pectate lyase 19 (At5g15110), Probable pectate lyase 3 (AT59), Probable pectate lyase 5 (At1g67750), Probable pectate lyase 6 (At2g02720), Probable pectate lyase 7 (At3g01270), Probable pectate lyase 8 (At3g07010), Probable pectate lyase 9 (At3g24230), Probable pectate lyase 12 (At3g53190), Putative pectate lyase 17 (At4g22090), Probable pectate lyase 10 (At3g24670), Probable pectate lyase 13 (PMR6), Probable pectate lyase 1 (At1g04680), Probable pectate lyase 20 (At5g48900), Probable pectate lyase 4 (At1g30350), Probable pectate lyase 16 (At4g22080), Probable pectate lyase 18 (At4g24780), Putative pectate lyase 21 (At5g55720), Probable pectate lyase 22 (At5g63180), Putative pectate lyase 2 (At1g11920), Putative pectate lyase 11 (At3g27400), Probable pectate lyase 15 (At4g13710), Pectate lyase (At5g09280), Pectate lyase (At3g55140), Pectate lyase, Pectate lyase (At1g14420), Pectate lyase (F11F8_12), Pectate lyase (At5g04310), Pectate lyase (AXX17_At3g47590), Pectate lyase (At3g09540), Pectate lyase (AXX17_At5g54880), Pectate lyase, Pectate lyase (AXX17_At5g08800), Pectate lyase (AXX17_At1g04020), Pectate lyase (AXX17_At1g15010), Pectate lyase (AXX17_At1g12300), Pectate lyase (At3g01270), Pectate lyase (AXX17_At2g01680), Pectate lyase (At3g55140), Pectate lyase (AXX17_At3g00310), Pectate lyase (AXX17_At5g47570), Pectate lyase (AXX17_At5g03700), Pectate lyase (AXX17_At1g30780), Pectate lyase (T26I12.20), Pectate lyase (AXX17_At3g29900), Pectate lyase (At3g07010), Pectate lyase (AXX17_At5g14600), Pectate lyase (AXX17_At1g61710), Pectate lyase (AXX17_At5g62760), Pectate lyase (At3g07010), Pectate lyase (At3g01270), Pectate lyase, Pectate lyase (AXX17_At4g25600), Pectate lyase (At5g04310), Pectate lyase (AXX17_At4g14900), Pectate lyase (AXX17_At4g15660), Pectate lyase (At3g53190), Pectate lyase, Pectate lyase (At4g13710), Pectate lyase (At4g13210), Pectate lyase (At3g07010), Pectate lyase (AXX17_At3g26720), Pectate lyase
  3. no protein annotated in this organism
  4. no protein annotated in this organism
  5. no protein annotated in this organism
This subpathway is part of the pathway pectin degradation, which is itself part of Glycan metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 2-dehydro-3-deoxy-D-gluconate from pectin, the pathway pectin degradation and in Glycan metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi206CalciumBy similarity1
Metal bindingi230CalciumBy similarity1
Metal bindingi234CalciumBy similarity1
Active sitei286Sequence analysis1

GO - Molecular functioni

GO - Biological processi

  • pectin catabolic process Source: UniProtKB-UniPathway
  • response to nematode Source: TAIR

Keywordsi

Molecular functionLyase
LigandCalcium, Metal-binding

Enzyme and pathway databases

BioCyciARA:AT4G24780-MONOMER
UniPathwayi
UPA00545;UER00824

Protein family/group databases

CAZyiPL1 Polysaccharide Lyase Family 1

Names & Taxonomyi

Protein namesi
Recommended name:
Probable pectate lyase 18 (EC:4.2.2.2)
Alternative name(s):
Pectate lyase A10
Gene namesi
Ordered Locus Names:At4g24780
ORF Names:F22K18.20
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

AraportiAT4G24780
TAIRilocus:2121914 AT4G24780

Subcellular locationi

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 24Sequence analysisAdd BLAST24
ChainiPRO_000002488325 – 408Probable pectate lyase 18Add BLAST384

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi42N-linked (GlcNAc...) asparagineSequence analysis1

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiQ9C5M8
PRIDEiQ9C5M8

Expressioni

Tissue specificityi

Expressed in flowers, but not in leaves.1 Publication

Gene expression databases

ExpressionAtlasiQ9C5M8 baseline and differential
GenevisibleiQ9C5M8 AT

Interactioni

Protein-protein interaction databases

BioGridi13869, 2 interactors
STRINGi3702.AT4G24780.1

Structurei

3D structure databases

ProteinModelPortaliQ9C5M8
SMRiQ9C5M8
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polysaccharide lyase 1 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG410IPFF Eukaryota
COG3866 LUCA
HOGENOMiHOG000237948
InParanoidiQ9C5M8
KOiK01728
OMAiAGAHNCK
OrthoDBiEOG09360CK2
PhylomeDBiQ9C5M8

Family and domain databases

Gene3Di2.160.20.10, 1 hit
InterProiView protein in InterPro
IPR018082 AmbAllergen
IPR002022 Pec_lyase
IPR012334 Pectin_lyas_fold
IPR011050 Pectin_lyase_fold/virulence
PfamiView protein in Pfam
PF00544 Pec_lyase_C, 1 hit
PRINTSiPR00807 AMBALLERGEN
SMARTiView protein in SMART
SM00656 Amb_all, 1 hit
SUPFAMiSSF51126 SSF51126, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9C5M8-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKMQTKKLFI TIVSFLLYAP LFLSSPVPDP ESVVEEVHKS INASVAGRRK
60 70 80 90 100
LGYLSCTTGN PIDDCWRCDP HWEQHRQRLA DCAIGFGKNA IGGRDGRIYV
110 120 130 140 150
VTDSGNDNPV SPKPGTLRHA VVQDEPLWII FQRDMTIQLK EELIMNSFKT
160 170 180 190 200
IDGRGASVHI SGGPCITIQY VTNIIIHGIH IHDCKQGGNA MVRSSPRHFG
210 220 230 240 250
WRTISDGDGV SIFGGSHVWV DHCSFSNCED GLIDAIMGST AITLSNNHMT
260 270 280 290 300
HHDKVMLLGH SDTYSRDKNM QVTIAFNHFG EGLVQRMPRC RHGYFHVVNN
310 320 330 340 350
DYTHWEMYAI GGSANPTINS QGNRFLAPNI RFSKEVTKHE DAPESEWKRW
360 370 380 390 400
NWRSSGDLLL NGAFFTPSGG AASSSYAKAS SLGAKPSSLV GPLTSTSGAL

NCRKGSRC
Length:408
Mass (Da):45,014
Last modified:June 16, 2003 - v2
Checksum:i4117CB52C48E588C
GO

Sequence cautioni

The sequence AAM65103 differs from that shown. Reason: Erroneous initiation.Curated
The sequence CAA22985 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence CAB79388 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti107D → Y in AAM65103 (Ref. 4) Curated1
Sequence conflicti252H → R in AAB69761 (PubMed:9278171).Curated1
Sequence conflicti271Q → H in AAK25850 (PubMed:14593172).Curated1
Sequence conflicti339H → D in AAM65103 (Ref. 4) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL035356 Genomic DNA Translation: CAA22985.1 Sequence problems.
AL161562 Genomic DNA Translation: CAB79388.1 Sequence problems.
CP002687 Genomic DNA Translation: AEE84955.1
CP002687 Genomic DNA Translation: AEE84956.1
AF360140 mRNA Translation: AAK25850.1
AY087561 mRNA Translation: AAM65103.1 Different initiation.
U83621 Genomic DNA Translation: AAB69761.1
PIRiT05556
RefSeqiNP_001190827.1, NM_001203898.1
NP_567707.1, NM_118611.3
UniGeneiAt.23543

Genome annotation databases

EnsemblPlantsiAT4G24780.1; AT4G24780.1; AT4G24780
AT4G24780.2; AT4G24780.2; AT4G24780
GeneIDi828580
GrameneiAT4G24780.1; AT4G24780.1; AT4G24780
AT4G24780.2; AT4G24780.2; AT4G24780
KEGGiath:AT4G24780

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL035356 Genomic DNA Translation: CAA22985.1 Sequence problems.
AL161562 Genomic DNA Translation: CAB79388.1 Sequence problems.
CP002687 Genomic DNA Translation: AEE84955.1
CP002687 Genomic DNA Translation: AEE84956.1
AF360140 mRNA Translation: AAK25850.1
AY087561 mRNA Translation: AAM65103.1 Different initiation.
U83621 Genomic DNA Translation: AAB69761.1
PIRiT05556
RefSeqiNP_001190827.1, NM_001203898.1
NP_567707.1, NM_118611.3
UniGeneiAt.23543

3D structure databases

ProteinModelPortaliQ9C5M8
SMRiQ9C5M8
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi13869, 2 interactors
STRINGi3702.AT4G24780.1

Protein family/group databases

CAZyiPL1 Polysaccharide Lyase Family 1

Proteomic databases

PaxDbiQ9C5M8
PRIDEiQ9C5M8

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G24780.1; AT4G24780.1; AT4G24780
AT4G24780.2; AT4G24780.2; AT4G24780
GeneIDi828580
GrameneiAT4G24780.1; AT4G24780.1; AT4G24780
AT4G24780.2; AT4G24780.2; AT4G24780
KEGGiath:AT4G24780

Organism-specific databases

AraportiAT4G24780
TAIRilocus:2121914 AT4G24780

Phylogenomic databases

eggNOGiENOG410IPFF Eukaryota
COG3866 LUCA
HOGENOMiHOG000237948
InParanoidiQ9C5M8
KOiK01728
OMAiAGAHNCK
OrthoDBiEOG09360CK2
PhylomeDBiQ9C5M8

Enzyme and pathway databases

UniPathwayi
UPA00545;UER00824

BioCyciARA:AT4G24780-MONOMER

Miscellaneous databases

PROiPR:Q9C5M8

Gene expression databases

ExpressionAtlasiQ9C5M8 baseline and differential
GenevisibleiQ9C5M8 AT

Family and domain databases

Gene3Di2.160.20.10, 1 hit
InterProiView protein in InterPro
IPR018082 AmbAllergen
IPR002022 Pec_lyase
IPR012334 Pectin_lyas_fold
IPR011050 Pectin_lyase_fold/virulence
PfamiView protein in Pfam
PF00544 Pec_lyase_C, 1 hit
PRINTSiPR00807 AMBALLERGEN
SMARTiView protein in SMART
SM00656 Amb_all, 1 hit
SUPFAMiSSF51126 SSF51126, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPLY18_ARATH
AccessioniPrimary (citable) accession number: Q9C5M8
Secondary accession number(s): O23667, Q8LAW7, Q9SB71
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 16, 2003
Last sequence update: June 16, 2003
Last modified: November 7, 2018
This is version 128 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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